“It is morally wrong, strategically unwise and, frankly, un-American to attempt to identify potentially dangerous immigrants based solely on their religion,” Dr. Tom Farr, president of the Religious Freedom Institute, stated to CNA.

However, he added, “a vigorous vetting can and should be done by applying sensible criteria, such as a history of violence, expressions of violent intent, or intentional association with terrorists.”

It is still not certain what Trump’s exact policy would be on immigration and travel from certain countries.

Last year, he called for a halt on any Muslims trying to enter the United States, in the wake of November terror attacks in Paris and a shooting in San Bernardino, Calif. by a Muslim couple who had become radicalized.

This summer, Trump proposed a ban on travel from countries “compromised” by terrorism. His running mate Mike Pence later said that ban would include Christian and Jewish refugees from those states.

One of Trump’s advisors on immigration, Kansas Secretary of State Kris Kobach, said recently that several immigration proposals were being sent to Trump for consideration, including one that would reinstate a controversial program started after the 9/11 attacks and suspended in 2011.

That program was the National Security Entry-Exit Registration System, started in the wake of the September 11, 2001 terror attacks. It instituted tougher security checks on non-citizen males ages 16 and over from certain countries deemed high-risk for terror.

Among other requirements, the men had to register with the U.S. government, agree to background checks and fingerprinting, and were monitored by authorities even after they arrived in the U.S.

Of the 25 countries on this list, 24 were Muslim-majority countries, one reason why critics like the ACLU charged that the program discriminated against Muslims. Because of strict penalties for failure to comply with the program, many men were deported for violating the requirements whether they were aware of them or not, the ACLU said. The Obama administration suspended the program in 2011.

No matter what program the Trump administration decides to implement, it must never register people simply based on their religion, religious freedom advocates maintain.

“If we believe in religious freedom and basic civil liberty we must reject any proposal for government to register people based on religion,” Robert George, former chair of the U.S. Commission on International Religious Freedom, tweeted last week.

The Trump transition team has insisted that any registry will not be based on religion, saying in a statement to CNN last week that “President-elect Trump has never advocated for any registry or system that tracks individuals based on their religion, and to imply otherwise is completely false.”

Yet, as the Washington Post documented, Trump either gave his assent to the idea of a Muslim registry or did not dismiss the idea on multiple occasions during the campaign.

When asked about the matter on NBC’s “Meet the Press” on Sunday, Reince Priebus, Trump’s incoming White House chief of staff, denied the administration would “have a registry based on a religion,” but added that there might be bans on immigration from some countries deemed high-risk for terror.

“Trump's position, is consistent with bills in the House and the Senate that say the following: If you want to come from a place or an area around the world that harbors and trains terrorists, we have to temporarily suspend that operation until a better vetting system is put in place,” Priebus explained.

Last year, after it was alleged that one of the perpetrators of the Paris terror attacks gained entry to the European Union by posing as a refugee, many, including members of Congress, Trump, and Pence, advocated that refugee resettlement from Syria be halted until the resettlement program was deemed secure.

Bills in the House and Senate were proposed that temporarily halted the Syrian resettlement program. Refugee resettlement experts, however, insisted that the system was secure and that the U.S. needed to continue and even increase its refugee intake given the record number of refugees around the globe.

Priebus acknowledged on Sunday that “Trump’s opinion is that there are some people within that particular religion [Islam] that we do fear.”

“But he has also made it very clear that we don’t believe in religious tests, and that we are not blanketly judging an entire religion, but in fact we will try to pinpoint the problems and temporarily suspend those areas from coming into the United States until a better vetting system is in place,” he continued.

Any policy cannot stigmatize Muslims, Farr said, noting that “stigmatizing an entire religion, and all its adherents, sends the wrong message to loyal American Muslims, as well as to Muslims abroad whose cooperation will be vital in winning the ideological war against violent Islamist extremism.”

Other comments about Muslims from Trump’s transition team have invited controversy, like past tweets from his new national security adviser, Ret. Lt. Gen. Michael Flynn.

“In next 24 hours, I dare Arab & Persian world 'leaders' to step up to the plate and declare their Islamic ideology sick and must B healed,” Flynn tweeted after a terror attack in Nice, France killed 86 people.

“Fear of Muslims is RATIONAL: please forward this to others: the truth fears no questions,” he tweeted of a video about Islam in February.

When asked by NBC’s Chuck Todd if Trump shared Flynn’s position that “fear of Muslims is rational,” Priebus said that “he [Flynn] believes that no faith in and of itself should be judged as a whole…but there are some that need to be prevented from coming into this country.”